The director of this program is on record saying that after deploying extensive analytical resources at the Pentagon onto all the evidence (cross referencing radar signatures, satellite feeds, etc) and leveraging internal expertise to rule out alternatives there remain cases for which there remains no explanation consistent with the idea that these are aircraft in any government's inventory or any other natural phenomena.
Either this person is lying, or somehow otherwise should be given no credibility, or the government has decided to reveal that there are in fact objects in the sky whose origin are, to the best of our country's ability to analyze them, unknown. This person specifically ruled out the idea in their NPR interview that these objects are part of some hidden government advanced aircraft program.
You can believe what you want to sleep better at night, such as that there is in fact some hyper-advanced tech the government has that this program was kept in the dark about, but there's not much wiggle room at this point other than to accept that the level of public acknowledgement of the UFO phenomena by the federal government (and particularly, the department of defense) has changed significantly now and that there is a very high prior that there are objects in the sky whose origins are a mystery.